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CSB
2005
IEEE
109views Bioinformatics» more  CSB 2005»
15 years 9 months ago
Patterns of Gene Deletion following Genome Duplication in Yeast
Whole genome duplication (WGD) is followed by massive duplicate deletion that reorganizes gene adjacencies. We compare the deletion patterns and adjacency reorganization following...
Jake K. Byrnes, Wen-Hsiung Li
126
Voted
CSB
2005
IEEE
129views Bioinformatics» more  CSB 2005»
15 years 9 months ago
A Pivoting Algorithm for Metabolic Networks in the Presence of Thermodynamic Constraints
A linear programming algorithm is presented to constructively compute thermodynamically feasible fluxes and change in chemical potentials of reactions for a metabolic network. It...
R. Nigam, S. Liang
122
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DNA
2001
Springer
164views Bioinformatics» more  DNA 2001»
15 years 8 months ago
A Clause String DNA Algorithm for SAT
A DNA algorithm for SAT, the satisfiability of propositional formulae, is presented where the number of separation steps is given by the number of clauses of the instance. This re...
Vincenzo Manca, Claudio Zandron
127
Voted
WABI
2001
Springer
124views Bioinformatics» more  WABI 2001»
15 years 7 months ago
Computing Linking Numbers of a Filtration
We develop fast algorithms for computing the linking number of a simplicial complex within a filtration. We give experimental results in applying our work toward the detection of...
Herbert Edelsbrunner, Afra Zomorodian
112
Voted
BIRD
2007
Springer
15 years 7 months ago
Fast Search Algorithms for Position Specific Scoring Matrices
Fast search algorithms for finding good instances of patterns given as position specific scoring matrices are developed, and some empirical results on their performance on DNA sequ...
Cinzia Pizzi, Pasi Rastas, Esko Ukkonen